Question: SRA to fastq
0
gravatar for aj123
2.8 years ago by
aj12370
United States
aj12370 wrote:

is there some way to convert SRA to fastq? im on a windows system and the sra toolkit is not working on my system.

sequencing next-gen fastq sra • 1.1k views
ADD COMMENTlink modified 18 days ago by i.sudbery2.4k • written 2.8 years ago by aj12370

You can try compiling the SRA toolkit under cygwin (didn't try, caveat emptor).

ADD REPLYlink written 2.8 years ago by vladimir.gritsenko70
3
gravatar for James Ashmore
2.8 years ago by
James Ashmore2.5k
UK/Edinburgh/MRC Centre for Regenerative Medicine
James Ashmore2.5k wrote:

You could upload your SRA files to Galaxy and use the SRA to FASTQ converter, however I'd strongly recommend you try to get the SRA toolkit working on your Windows machine.

ADD COMMENTlink written 2.8 years ago by James Ashmore2.5k
2
gravatar for Being Bioinformatician
2.8 years ago by
India
Being Bioinformatician130 wrote:

At first check your system specification . Download SRA toolkits accordingly(32 bits/ 64 bits) 

That might solve the problem

ADD COMMENTlink written 2.8 years ago by Being Bioinformatician130
1
gravatar for ATpoint
18 days ago by
ATpoint5.7k
Germany
ATpoint5.7k wrote:

There is now a new release of the SRAtoolkit (2.9.1) that introduces fasterq-dump, a multithreaded follow-up of fastq-dump. Had a quick look at it and the increase in speed is notable, but (and I really do not understand this in 2018 at all) there is no longer a --gzip option, requiring additional post-processing. I really do not understand why, in times where projects may require the processing of terabytes of .sra data, a tool can lack a compression option, flooding the hard drives with Tb of unnecessarily large amounts of data (the last sentence is of course thinking aloud). I will probably stick with parallel-fastq-dump, given that files (e.g. from dbGaP) are not backed up on ENA.

ADD COMMENTlink modified 18 days ago • written 18 days ago by ATpoint5.7k
1
gravatar for i.sudbery
18 days ago by
i.sudbery2.4k
Sheffield, UK
i.sudbery2.4k wrote:

Not quite an answer to the question you are asking, but the ENA (European Nucleotide Archive) has all publically available SRA samples for download directly as fastq. The download will take much longer (unless you use aspera), but the you more than make up for it in conversion time.

ADD COMMENTlink written 18 days ago by i.sudbery2.4k

And ENA makes it easier to retrieve the metadata as well, for both human and machine consumption.

ADD REPLYlink written 17 days ago by igor6.3k
0
gravatar for arunprasanna83
15 months ago by
arunprasanna8320 wrote:

From SRA toolkit => "./fastq-dump SRA* "

ADD COMMENTlink written 15 months ago by arunprasanna8320
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